Contacts of the helix formed by residues 240 - 255 (chain C) in PDB entry 1C2O
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 240 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239C VAL* 1.3 78.4 - - - +
241C ALA* 1.3 64.9 + - - +
242C GLY* 3.8 4.8 + - - -
243C GLU* 3.3 22.1 + - - +
244C ALA* 3.0 21.7 + - - +
302C VAL* 3.8 2.5 - - - -
303C VAL* 4.7 8.5 - - - +
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Residues in contact with ALA 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C PRO* 3.6 32.8 - - + +
240C SER* 1.3 73.6 - - - +
242C GLY* 1.3 66.9 + - - +
244C ALA* 2.8 4.3 + - - +
245C ARG* 2.7 23.5 + - - +
302C VAL* 3.8 9.6 - - + +
303C VAL 4.2 12.8 + - - +
304C ASP* 5.7 0.9 - - - -
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Residues in contact with GLY 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C SER* 3.4 6.2 + - - -
241C ALA* 1.3 79.4 - - - +
243C GLU* 1.3 55.9 + - - +
245C ARG* 3.4 7.4 + - - +
246C ARG* 2.9 27.6 + - - +
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Residues in contact with GLU 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C VAL* 4.4 6.1 - - + -
240C SER* 3.3 24.7 + - - +
241C ALA 3.2 0.4 - - - -
242C GLY* 1.3 74.0 - - - +
244C ALA* 1.3 58.9 - - - +
246C ARG* 2.6 46.9 + - - +
247C ARG* 2.5 83.5 + - - +
290C PRO* 3.8 8.3 - - - +
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Residues in contact with ALA 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C ALA* 3.8 18.8 + - + +
162C PRO* 4.1 4.0 - - + -
239C VAL* 4.1 10.3 - - + -
240C SER 3.0 13.8 + - - +
241C ALA* 2.8 10.1 + - - +
243C GLU* 1.3 75.3 - - - +
245C ARG* 1.3 68.5 + - - +
247C ARG* 2.8 8.9 + - - +
248C ALA* 2.7 22.9 + - - +
299C PHE* 5.0 3.9 - - - -
302C VAL* 3.8 21.8 - - + -
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Residues in contact with ARG 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C ALA 3.9 9.6 + - - -
161C LEU* 3.2 37.2 - - - +
162C PRO* 4.1 14.5 + - + +
241C ALA 2.7 15.3 + - - +
242C GLY* 3.5 10.5 - - - +
244C ALA* 1.3 74.3 - - - +
246C ARG* 1.3 65.7 + - - +
248C ALA* 2.8 13.9 + - - -
249C THR* 3.0 36.6 + - + +
264C GLY* 6.2 1.8 - - - -
266C ASP* 3.1 25.2 + - - -
269C LEU* 5.5 0.6 - - - +
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Residues in contact with ARG 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C GLY 2.9 18.6 + - - +
243C GLU* 2.6 54.3 + - - +
244C ALA 3.2 0.2 - - - -
245C ARG* 1.3 77.4 - - - +
247C ARG* 1.4 63.4 + - - +
249C THR* 3.3 5.1 + - - -
250C LEU* 3.1 52.7 + - + +
288C VAL 2.8 30.9 + - - -
289C LEU 4.0 6.3 + - - -
290C PRO* 3.5 20.2 - - - +
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Residues in contact with ARG 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C VAL* 3.9 22.2 - - - +
243C GLU* 2.5 53.3 + - - +
244C ALA* 2.8 4.5 + - - +
246C ARG* 1.4 90.5 - - - +
248C ALA* 1.3 61.0 + - - +
250C LEU* 3.9 1.3 - - - +
251C LEU* 3.0 28.2 + - - +
288C VAL* 3.4 30.3 - - + +
289C LEU* 3.5 16.8 - - - +
290C PRO* 3.6 19.7 - - - +
296C ARG* 5.6 4.4 - - - +
297C PHE 3.0 27.5 + - - -
298C SER 3.0 23.9 + - - -
299C PHE* 3.5 11.4 - - + -
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Residues in contact with ALA 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C LEU* 4.0 16.2 - - + +
160C ALA 3.4 26.2 - - - +
161C LEU* 3.6 21.8 - - + -
244C ALA 2.7 13.5 + - - +
245C ARG* 2.8 5.0 + - - +
247C ARG* 1.3 70.5 - - - +
249C THR* 1.3 57.3 + - - +
251C LEU* 2.9 5.4 + - - +
252C ALA* 2.6 36.2 + - - +
273C LEU* 5.6 0.4 - - - -
299C PHE* 4.3 8.7 - - - -
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Residues in contact with THR 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C LEU* 5.0 0.4 - - + +
245C ARG* 3.4 43.6 + - + +
246C ARG* 3.3 10.9 + - - -
248C ALA* 1.3 80.2 - - + +
250C LEU* 1.3 76.5 + - - +
252C ALA* 3.0 9.2 + - - +
253C ARG* 2.7 44.2 + - - +
269C LEU* 4.3 18.2 - - + -
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Residues in contact with LEU 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C ARG* 3.1 42.5 + - + +
249C THR* 1.3 85.3 + - - +
251C LEU* 1.3 65.1 + - - +
253C ARG* 3.2 30.5 + - + +
254C LEU* 2.9 38.4 + - + +
287C HIS 3.8 11.2 - - - +
288C VAL* 3.6 23.1 - - + -
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Residues in contact with LEU 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C THR* 3.9 16.8 - - + -
159C LEU* 4.0 11.4 - - + -
247C ARG 3.0 19.3 + - - +
248C ALA 2.9 3.6 + - - +
250C LEU* 1.3 77.6 - - - +
252C ALA* 1.3 69.5 + - - +
254C LEU* 3.1 14.2 + - - +
255C VAL* 3.3 10.4 + - + +
273C LEU* 4.0 2.9 - - + -
281C LEU* 3.6 36.8 - - + +
284C HIS* 3.5 42.6 - - + +
285C GLU* 3.7 9.4 - - - +
288C VAL* 3.6 8.5 - - + +
299C PHE* 4.2 13.2 - - + -
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Residues in contact with ALA 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C ALA 2.6 15.5 + - - +
249C THR* 3.4 8.1 - - - +
251C LEU* 1.3 74.5 - - - +
253C ARG* 1.3 53.9 + - - +
255C VAL* 2.7 25.9 + - - +
256C GLY 3.1 0.2 + - - -
257C CYS* 2.9 31.3 + - + +
269C LEU* 3.2 30.1 - - + -
273C LEU* 3.8 21.3 - - + -
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Residues in contact with ARG 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C THR* 2.7 38.1 + - - +
250C LEU* 3.4 42.6 - - + +
252C ALA* 1.3 71.8 - - - +
254C LEU* 1.3 64.8 + - + +
256C GLY* 2.9 15.0 + - - -
257C CYS 3.0 11.5 + - - +
258C PRO* 5.3 7.1 - - + +
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Residues in contact with LEU 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C LEU* 2.9 38.9 + - + +
251C LEU* 3.1 7.6 + - - +
253C ARG* 1.3 75.1 - - + +
255C VAL* 1.3 57.6 + - - +
256C GLY 3.3 1.5 + - - -
284C HIS* 3.7 50.7 + - + +
287C HIS* 3.9 23.6 - - + +
288C VAL* 4.8 3.8 - - + -
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Residues in contact with VAL 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C LEU 3.3 7.6 + - - +
252C ALA 2.7 18.1 + - - +
254C LEU* 1.3 74.5 - - - +
256C GLY* 1.3 56.4 + - - +
257C CYS* 4.0 4.0 - - - +
273C LEU* 4.0 20.6 - - + -
276C ARG* 2.8 51.4 + - + +
280C ASP* 3.8 42.2 - - + +
281C LEU* 4.1 9.4 - - + -
284C HIS* 4.2 11.0 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il